Helices in Proteins

From Proteopedia

Jump to: navigation, search

Helical conformations in proteins

This page illustrates the 3 most common helical conformations (among secondary structures) found in proteins.

Each of the three examples below is a decapeptide fragment extracted from an actual protein structure in the PDB. They are shown using the same scale, for a better comparison (as a consequence, zoom in the Jmol applets is disabled).

(For optimal results you should act with your mouse on the leftmost model)

To re-align the 3 models, either reload this page or uncheck the synchronization and click on each of the 3 green 'Reset' links.

310 helix alpha helix pi helix


3 residues/turn
rise 0.20 nm/residue
helix pitch 0.60 nm
H bonds: Ni+3 → Oi
φ = -49°, ψ = -26°
3l79: 514-525


3.6 residues/turn
rise 0.15 nm/residue
helix pitch 0.54 nm
H bonds: Ni+4 → Oi
φ = -60°, ψ = -45°
1hho chain B: 5-16


4.4 residues/turn
rise ~0.115 nm/residue
helix pitch ~0.41 nm
H bonds: Ni+5 → Oi
φ = -55°, ψ = -70° (approx.)
2qd3 chain A: 346-357

The alpha helix is by far the most common helix. Note that it is a right-handed helix when formed with the common L-amino acids[1][2][3]. (It is left-handed when formed with D-amino acids[1][2][3].) When viewed from either end, right-handed helices turn clockwise when followed away from you.

See Also

References

  1. 1.0 1.1 Novotny M, Kleywegt GJ. A survey of left-handed helices in protein structures. J Mol Biol. 2005 Mar 25;347(2):231-41. PMID:15740737 doi:10.1016/j.jmb.2005.01.037
  2. 2.0 2.1 Jourdan F, Lazzaroni S, Mendez BL, Lo Cantore P, de Julio M, Amodeo P, Iacobellis NS, Evidente A, Motta A. A left-handed alpha-helix containing both L- and D-amino acids: the solution structure of the antimicrobial lipodepsipeptide tolaasin. Proteins. 2003 Sep 1;52(4):534-43. PMID:12910453 doi:http://dx.doi.org/10.1002/prot.10418
  3. 3.0 3.1 Moradi M, Babin V, Roland C, Darden TA, Sagui C. Conformations and free energy landscapes of polyproline peptides. Proc Natl Acad Sci U S A. 2009 Dec 8;106(49):20746-51. Epub 2009 Nov 18. PMID:19923435 doi:10.1073/pnas.0906500106

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Angel Herraez

Personal tools